IIRC the seed has always derived 2 out of 3 keys (I could be wrong here, but i am relatively sure it has always been this way).
If you create a new wallet with 2FA enabled the wallet file just stores one of these 2 keys.
But if you decide to create it as a wallet with 2FA disabled, it will store both of the keys (which allos to sign transactions).
A while ago, there used to be a 24 word seed. I think this has probably been broken down a bit simpler (as everone kept losing their 24 word seed and there's not really much point in having two when you can do the same in one).
I always thought - supidly - that you have to input the same key that gets generated that you can then send to TrustedCoin (I must have gotton confused - yet again - somewhere).
this thread is where I first became confused as to these 2FA wallets.
2FA is basically a multisignature wallet with 3 keys and needing 2 keys to sign (2 of 3 multi-sig). there are in fact 3 master private keys being generated. you create 2 of them and TrustedCoin creates the other one (the 3rd one). it doesn't matter how many words your seed has or whether it shows these words or not, when you create a new 2FA wallet you create 2 master private keys and send the public key to TrustedCoin, then they create another master private key and send you the public key so the wallet is completed.
now what you store in your wallet file is a little different here. with a regular wallet you have a seed that generates all your private keys so you store that in your wallet file.
with a 2FA wallet you want to only store 1 key so that if your wallet is compromised it still requires the third party (TrustedCoin) key to spend the coins you have so you only store that 1 master private key instead of the seed which is 2 keys.
in the end there are always 3 keys:
1. master private key stored in your wallet file and used for half signing the transactions
2. master private key generated from your seed but neither your seed nor this key are stored in your wallet file, you have to write down your seed. your wallet only stores the master public key of this.
3. master private key generated by TrustedCoin and stored on their servers used to half sign the transactions